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ingest/build-configs/nextstrain-automation: Add README
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# Nextstrain automation | ||
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> [!NOTE] | ||
> External users can ignore this directory! | ||
> This build config/customization is tailored for the internal Nextstrain team | ||
> to extend the core ingest workflow for automated workflows. | ||
## Update the config | ||
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Update the [config.yaml](config.yaml) for your pathogen: | ||
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1. Edit the `s3_dst` param to add the pathogen repository name. | ||
2. Edit the `files_to_upload` param to a mapping of files you need to upload for your pathogen. | ||
The default includes suggested files for uploading curated data and Nextclade outputs. | ||
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## Run the workflow | ||
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Provide the additional config file to the Snakemake options in order to | ||
include the custom rules from [upload.smk](upload.smk) in the workflow. | ||
Specify the `upload_all` target in order to run the additional upload rules. | ||
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The upload rules will require AWS credentials for a user that has permissions | ||
to upload to the Nextstrain data bucket. | ||
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The customized workflow can be run from the top level pathogen repo directory with: | ||
``` | ||
nextstrain build \ | ||
--env AWS_ACCESS_KEY_ID \ | ||
--env AWS_SECRET_ACCESS_KEY \ | ||
ingest \ | ||
upload_all \ | ||
--configfile build-configs/nextstrain-automation/config.yaml | ||
``` | ||
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## Automated GitHub Action workflows | ||
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Additional instructions on how to use this with the shared `pathogen-repo-build` | ||
GitHub Action workflow to come! |